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NMF (version 0.20.5)

Algorithms and framework for Nonnegative Matrix Factorization (NMF)

Description

This package provides a framework to perform Non-negative Matrix Factorization (NMF). It implements a set of already published algorithms and seeding methods, and provides a framework to test, develop and plug new/custom algorithms. Most of the built-in algorithms have been optimized in C++, and the main interface function provides an easy way of performing parallel computations on multicore machines.

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Version

Install

install.packages('NMF')

Monthly Downloads

10,233

Version

0.20.5

License

GPL (>= 2)

Maintainer

Renaud Gaujoux

Last Published

March 18th, 2014

Functions in NMF (0.20.5)

.atrack

Annotation Tracks
summary

Assessing and Comparing NMF Models
algorithmic-NMF

Generic Interface for Algorithms
getRNG1

Extracting RNG Data from NMF Objects
consensus,NMFfitXn-method

Computes the consensus matrix of the set of fits stored in object, as the mean connectivity matrix across runs.
registerDoBackend

Utilities and Extensions for Foreach Loops
fcnnls

Fast Combinatorial Nonnegative Least-Square
parallel-NMF

Utilities for Parallel Computations
cluster_mat

Cluster Matrix Rows in Annotated Heatmaps
tryViewport

Internal Grid Extension
parse_formula

Simple Parsing of Formula
nmf_update.euclidean_offset.h

NMF Multiplicative Update for NMF with Offset Models
rmatrix

Generating Random Matrices
show,NMFfitX-method

Show method for objects of class NMFfitX
show,NMFStrategyIterative-method

Show method for objects of class NMFStrategyIterative
canFit

Testing Compatibility of Algorithm and Models
NMFSeed-class

Base class that defines the interface for NMF seeding methods.
nmf_update.lee_R

NMF Algorithm/Updates for Frobenius Norm
consensus,NMFfitX1-method

Returns the consensus matrix computed while performing all NMF runs, amongst which object was selected as the best fit.
.fcnnls

Internal Routine for Fast Combinatorial Nonnegative Least-Squares
nmf.equal

Testing Equality of NMF Models
pmax.inplace

Updating Objects In Place
nmfAlgorithm

Listing and Retrieving NMF Algorithms
nmfWrapper

Wrapping NMF Algorithms
dispersion

Dispersion of a Matrix
seed

Interface for NMF Seeding Methods
scale.NMF

Rescaling NMF Models
t.NMF

Transformation NMF Model Objects
silhouette.NMF

Silhouette of NMF Clustering
sparseness

Sparseness
show,NMFList-method

Show method for objects of class NMFList
utils-NMF

Utility Function in the NMF Package
cutdendro

Fade Out the Upper Branches from a Dendrogram
advanced-NMF

Advanced Usage of the Package NMF
match_atrack

Extending Annotation Vectors
nmfEstimateRank

Estimate Rank for NMF Models
nneg

Transforming from Mixed-sign to Nonnegative Data
methods-NMF

Registry for NMF Algorithms
smoothing

Smoothing Matrix in Nonsmooth NMF Models
syntheticNMF

Simulating Datasets
bterms<-

Fixed Terms in NMF Models
bioc-NMF

Specific NMF Layer for Bioconductor
NMF-class

Generic Interface for Nonnegative Matrix Factorisation Models
c,NMF-method

Concatenating NMF Models
ccSpec

Extract Colour Palette Specification
nmfCheck

Checking NMF Algorithm
deviance

Distances and Objective Functions
NMFStop

Stopping Criteria for NMF Iterative Strategies
nmfSeed

Seeding Strategies for NMF Algorithms
nmf_update.euclidean.h

NMF Multiplicative Updates for Euclidean Distance
NMFStrategyFunction-class

Interface for Single Function NMF Strategies
NMFfitX

Factory Method for Multiple NMF Run Objects
aheatmap

Annotated Heatmaps
basiscor

Correlations in NMF Models
consensushc

Hierarchical Clustering of a Consensus Matrix
fit

Extracting Fitted Models
cophcor

Cophenetic Correlation Coefficient
offset,NMFfit-method

Returns the offset from the fitted model.
options-NMF

NMF Package Specific Options
residuals

Residuals in NMF Models
featureScore

Feature Selection in NMF Models
staticVar

Get/Set a Static Variable in NMF Algorithms
show,NMFfitXn-method

Show method for objects of class NMFfitXn
ibterms

Fixed Terms in NMF Models
NMF-deprecated

Deprecated Functions in the Package NMF
NMFStrategy

Factory Method for NMFStrategy Objects
NMF-package

Algorithms and framework for Nonnegative Matrix Factorization (NMF).
NMFfitX-class

Virtual Class to Handle Results from Multiple Runs of NMF Algorithms
NMFStrategyOctave-class

S4 Interface for Octave-Matlab NMF Algorithms
basis

Accessing NMF Factors
nmfFormals

Showing Arguments of NMF Algorithms
objective,NMFfit-method

Returns the objective function associated with the algorithm that computed the fitted NMF model object, or the objective value with respect to a given target matrix y if it is supplied.
nmfReport

Run NMF Methods and Generate a Report
plot,NMFfit,missing-method

Plots the residual track computed at regular interval during the fit of the NMF model x.
ccRamp

Builds a Color Ramp from Compact Color Specification
setNMFMethod

Registering NMF Algorithms
show,NMFSeed-method

Show method for objects of class NMFSeed
show,NMFfitX1-method

Show method for objects of class NMFfitX1
show,NMFns-method

Show method for objects of class NMFns
txtProgressBar

Simple Progress Bar
nmfAlgorithm.SNMF_R

NMF Algorithm - Sparse NMF via Alternating NNLS
NMFOffset-class

NMF Model - Nonnegative Matrix Factorization with Offset
algorithm,NMFList-method

Returns the method names used to compute the NMF fits in the list. It returns NULL if the list is empty.
connectivity

Clustering Connectivity and Consensus Matrices
basisnames

Dimension names for NMF objects
nmf

Running NMF algorithms
nmf_update.lsnmf

Multiplicative Updates for LS-NMF
nmfObject

Updating NMF Objects
nmfApply

Apply Function for NMF Objects
randomize

Randomizing Data
revPalette

Flags a Color Palette Specification for Reversion
compare-NMF

Comparing Results from Different NMF Runs
show,NMF-method

Show method for objects of class NMF
nmfModel

Factory Methods NMF Models
NMFList-class

Class for Storing Heterogeneous NMF fits
nmf_update.brunet_R

NMF Algorithm/Updates for Kullback-Leibler Divergence
NMFfitX1-class

Structure for Storing the Best Fit Amongst Multiple NMF Runs
NMFStrategyIterative-class

Interface for Algorithms: Implementation for Iterative NMF Algorithms
NMFfitXn-class

Structure for Storing All Fits from Multiple NMF Runs
esGolub

Golub ExpressionSet
gfile

Open a File Graphic Device
fitted

Fitted Matrix in NMF Models
nmf_update.KL.h

NMF Multiplicative Updates for Kullback-Leibler Divergence
setupBackend

Computational Setup Functions
[,NMF-method

Sub-setting NMF Objects
NMFfit-class

Base Class for to store Nonnegative Matrix Factorisation results
NMFstd-class

NMF Model - Standard model
NMFns-class

NMF Model - Nonsmooth Nonnegative Matrix Factorization
ccPalette

Builds a Color Palette from Compact Color Specification
nbasis

Dimension of NMF Objects
offset,NMFOffset-method

Offsets in NMF Models with Offset
ccBreaks

Generate Break Intervals from Numeric Variables
lverbose

Internal verbosity option
purity

Purity and Entropy of a Clustering
profplot

Plotting Expression Profiles
rnmf

Generating Random NMF Models
runtime.all,NMFfitXn-method

Returns the CPU time used to perform all the NMF fits stored in object.
show,NMFfit-method

Show method for objects of class NMFfit
is.nmf

Testing NMF Objects
algorithm,NMFStrategyOctave-method

Returns the name of the Octave/Matlab function that implements the NMF algorithm -- as stored in slot algorithm.
heatmap-NMF

Heatmaps of NMF Factors
rss

Residual Sum of Squares and Explained Variance
show,NMFOffset-method

Show method for objects of class NMFOffset
NMF-defunct

Defunct Functions and Classes in the NMF Package
nmf_update.ns

NMF Multiplicative Update for Nonsmooth Nonnegative Matrix Factorization (nsNMF).
Strategy-class

Generic Strategy Class
checkErrors

Error Checks in NMF Runs
runtime,NMFList-method

Returns the CPU time required to compute all NMF fits in the list. It returns NULL if the list is empty. If no timing data are available, the sequential time is returned.
NMFStrategy-class

Virtual Interface for NMF Algorithms
predict

Clustering and Prediction